We would like to thank The Company of Biologists for additional funding of the EMBO practical course on measuring translational dynamics by ribosome profiling to be held at the Advanced Training Centre at the European Molecular Biology Laboratory (EMBL) in Heidelberg from March 26th to April 1st.
Are you interested in establishing ribosome profiling in your lab to analyze cellular translation comprehensively and quantitatively?
Check out our novel and simplified protocol! The standardized workflow employs an extremely rapid sequencing library preparation protocol (12 hours) that relies on solid phase extraction of reaction intermediates, making it easy to implement in any standard laboratory. The protocol yields data of extremely high quality from minute amounts input material allowing the analysis of samples that were previously not easily amenable to this type of experimentation.
Access the preprint on bioRxiv here
If you are interested in practical training on how to perform the experiments, make sure to apply for a spot in the EMBO Practical Course on Measuring translational dynamics by ribosome profiling (March 26 – April 1 2023 at EMBL Heidelberg)
Good news: the website is up – click here!
The course will be held at the Advanced training centre at EMBL in Heidelberg from March 26th to April 1st. Get your CVs ready, as registration will open soon (registration deadline: January 30th)!
Stay tuned for updates!
We are very happy to announce that our funding application for a second round of the EMBO Practical Course Measuring translational dynamics by ribosome profiling has been successful!
On behalf of all organizers, I would like to thank the expert speakers that have agreed to support the course: Nicholas Ingolia, Rachel Green, Anne Willis, Marina Rodnina, Noam Stern-Ginossar, Michael VanInsberghe, and Vladimir Benes.
The course will take place from March 26th to April 1st at the Advanced Training Centre (ATC) at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany. We are very much looking forward to your applications and a week packed full of exciting science and labwork! Stay tuned and/or check the official webpage for updates and details.
Our study of the activity of tha TRIM-NHL protein Mei-P26, a regulator of cell fate in Drosophila, has now been published at Life Science Alliance (doi 10.26508/lsa.202201418).
In a close collaboration with the labs of Sebastian Glatt (Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University Krakow, Poland) and Janusz Bujnicki (Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Poland), we could solve the first high resolution structure of the Mei-P26 NHL domain and define a consensus RNA motif that it recognizes. Molecular dynamics simulations allowed us to predict and subsequently experimentally validate key amino acid residues involved specific RNA recognition, highlighting differences to other NHL domains. Using individual nucleotide resolution cross-linking and immunoprecipitation (iCLIP), we could identify RNA targets of Mei-P26 in cultured Drosophila cells and demonstrate the protein can either repress or activate its genuine mRNA targets. Regulation requires the NHL domain of the protein but is independent of its function as a ubiquitin ligase.
In particular, the last finding significantly expands our understanding of TRIM-NHL protein-mediated gene regulation. These proteins were previously considered to exclusively act as repressors of gene expression. Strikingly, Mei-P26 itself appears to lack any regulatory activity suggesting that the regulatory outcome is determined by the recruitment of different co-factors, some of which have previously been identified.
We had an exciting time during the practical course on rapid and high sensitivity analyses of cellular translation by ribosome profiling. 13 international participants joined us in Regensburg for a five day lab course during which they very successfully prepared ribsome profiling libraries from a human cell line using only minute amounts of input material.
We would like to thank all participants for their enthusiasm and for sharing with us insight into their exciting research projects! We had a great time working together and discussion science with you.
We also thank Sebastian Leidel (Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Switzerland) and Thomas Preiss (John Curtin School of Medical Research at the Australia National University, Australia) for supporting the course with exciting lectures and for contributing expert opinions and insight into the challenges and pitfalls of performing ribosome profiling experiments.
We are grateful for the support by the Graduate Research Academy RNA Biology of the Collaborative Research Center SFB 960 and siTOOLs Biotech.
Dear participants, please find some information on the practical course on ribosome profiling here. The information will be frequently updated… Looking forward to meeting you in Regensburg!
I would like to bring to your attention the following practical course which we will host in Regensburg from April 25th to 29th: 2022:
This hands-on course will teach how to generate comprehensive and quantitative snapshots of cellular translation from minute amounts of sample. Starting from cultured cells, ribosome-protected fragments will be produced, purified, and subjected to sequencing library preparation using a streamlined protocol which is optimized for small amounts of input. Detailed background information will be provided on (1) the optimization and adaptation of ribosome profiling to different model systems and research questions, (2) state-of-the-art sequencing library preparation, and (3) the bioinformatic analyses of ribosome profiling data.
Guest speakers will be: Sebastian Leidel (Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Switzerland) and Thomas Preiss (John Curtin School of Medical Research at the Australia National University, Australia)
Apply by March 27th with your CV and a letter of motivation to info@rnabiology-regensburg.de. There are no registration fees!
This course is supported by the graduate school of the Graduate School RNA Biology of the Collaborative Research Centre 960 (SFB960) – RNP biogenesis: assembly of ribosomes and non-ribosomal RNPs and control of their function
Pünktlich zum Weltkrebstag, dem 04. Februar, erscheint eine Pressemitteilung über unsere Forschungsergebnisse. Gemeinsam mit unseren Partnern Robert Ahrends, Grischa Tödt, Björn Tews und Christiane Knobbe-Thomsen, haben wir einen neuen Mechanismus entdeckt, der in Tumorzellen eine Resistenz gegen weit verbreitete Chemotherapeutika auslöst. Diese Chemoresistenz hat dramatische Folgen für betroffene Patienten, da die Behandlung stark eingeschränkt wird. Ein besseres Verständnis des Mechanismus der Chemoresistenz soll zukünftig neue Therapieoptionen ermöglichen.
Gefördert wurde die Forschungsarbeit im SUPR-G (Systems Biology of the Unfolded Protein Response in Glioma) Konsortium durch das Bundesministerium für Bildung und Forschung (BMBF) im Rahmen der e:med Initiative (Maßnahmen zur Etablierung der Systemmedizin).
From January 17th to 21st, we will run a practical course on ribosome profiling at the Justus-Liebig-University in Gießen. Focusing on our newly-developed and high-sensitivity protocol, we will teach students of the DFG-funded Research Training Group 2355 ‘Regulatory networks in the mRNA life cycle: from coding to non-coding RNAs’ how to analyze cellular translation using ribosome profiling. We are very much looking forward to the course and to introducing our ultra-rapid protocol to our colleagues for the first time.
Markus Romberger has joined the lab. He will employ our newly developed and improved ribosome profiling protocol to address how cellular stress remodels translation. Welcome to the lab!
The TRIM-NHL protein Meiotic-P26 acts as a regulator of cell fate in Drosophila. Its activity is critical for ovarian germline stem cell maintenance, differentiation of oocytes and spermatogenesis. Together with our collaborators from the Glatt lab (Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University Krakow, Poland) and the Bujnicki lab (Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Poland), we could solve the first high resolution structure of the Mei-P26 NHL domain and define a consensus RNA motif that it recognizes. Molecular dynamics simulations allowed us to predict and subsequently experimentally validate key amino acid residues involved specific RNA recognition, highlighting differences to other NHL domains. Using individual nucleotide resolution cross-linking and immunoprecipitation (iCLIP), we could identify RNA targets of Mei-P26 in cultured Drosophila cells and demonstrate the protein can either repress or activate its genuine mRNA targets. Regulation requires the NHL domain of the protein but is independent of its function as a ubiquitin ligase.
In particular, the last finding significantly expands our understanding of TRIM-NHL protein-mediated gene regulation. These proteins were previously considered to exclusively act as repressors of gene expression. Strikingly, Mei-P26 itself appears to lack any regulatory activity suggesting that the regulatory outcome is determined by the recruitment of different co-factors, some of which have previously been identified by genetic means.
A preprint of the manuscript is available at bioRxiv (doi.org/10.1101/2021.09.20.461029)
On Tuesday, July 20th Andreas Horn very successfully defended his PhD thesis. For many years, Andreas was advancing our understanding of how RNA binding proteins control development and cell fate decisions in the model organism Drosophila melanogaster. We are very proud and happy about Andreas’ success and we wish him all the best for his future endeavors.
After being postponed due to the Coronavirus pandemic, the EMBO practical course on measuring translational dynamics by ribosome profiling could finally take place from May 17th to 25th 2021 in a virtual format. 16 participants from research labs across the globe discussed intensively with ten speakers and 12 trainers about how to perform ribosome profiling experiments. Pre-recorded talks provided insight into the different aspects of the technique and used recent examples to illustrate how ribosome profiling can be used to further our understanding of translation and its regulation. Furthermore, Pavel ‘Pasha’ Baranov and his team from the University College Cork provided an excellent online tutorial on the bioinformatic analyses of ribosome data.
I am particular grateful for the insightful talks provided by Nicholas Ingolia (UC Berkeley), Marina Rodnina (MPI Göttingen), Rachel Green (Johns Hopkins), Anne Willis (University of Cambridge), Thomas Preiss (Australia National University), Gerben Menschaert (Ghent University), and Vladimir Benes (EMBL Heidelberg) that made the curse a big success. Also, on behalf of all organizers, I would like to thank Lisa Trinh, Diah Yulianti, Irena Provaznikova (from the EMBL Courses and Conferences Office) and in particular Yvonne Yeboah (form the EMBL teaching lab) for their daily support. Finally, without the expertise of my co-organizers Elisabeth Zielonka (EMBL Heidelberg), Sebastian Leidel (University of Bern), and Pavel ‘Pasha’ Baranov (University College Cork) it would not have been possible to host this course.
Above: Short explanatory movie on ribosome profiling. I would like to thank Daniel Krüger, Julia Schleisiek, Claudiu Grozea, and in particular Yvonne Yeboah and Sebastian Leidel for production of the video. More information on the movie can be found here.
Are you excited about biomedical research? Do you want to employ state-of-the-art methodology with the aim to unerstand how tumor cells become resistant to treatment? Do you want to work in a stimulating research environment with great colleagues? Then this is the right job for you:
We are looking for a Technical Assistant to perform ribosome profiling experiments in the context of cellular stress and resistance to chemotherapeutic treatment. Click here for more information (PDF, german).
Please feel free to contact us any time for more details…
